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Looking to your pano when it is self turning I get squared blurry blocks in between which are not sharp. Are you sure you shave set lens and camera body to manual at focus? Did you tape the focus ring?

With longer focal length lenses, you may not be able to accommodate the full depth of field of the scene with the lens at one focus setting. If necessary, you can shoot each row with a different focus setting. Changing the focus setting alters the fov, so you need to take account of this in the stitching. In PTGui, you can assign individual lens parameters (FOV) on the Lens Details tab. Do this for all rows other than the main horizontal row. You can use the advanced optimizer tab to optimize the rows individually or all together, as you like.

You shoot the spherical panorama with 8 rows with different detent plunger settings = small blue knob of RD16 which gives you different numbers of stops. Each detent setting is related to a number of stops.
For each row you have to set the upper rail to a different pitch = moving the upper rail up or down to a certain angleº.

Now first shot +90º for zenith.

1.row: detend plunger set to 24º = 15 Stops, upper rail set to +72,5º Pitch: begin at 0º , turn to the right to the next stop, and take a shot at every single stop.

2.row: detend plunger set to 18º = 20 Stops, upper rail set to +52.2º Pitch: shot all the 20 stops, and reset the settings for the next row, and so on. For the rows with 12º = 30 stops you only change the pitch for the next row.

At least shoot the two Nadir shots -90º if you have a NN Nadir Adapter or a normal plus a handheld one.

If you end up with gaps in between shots to stitch, tell me and I will send a table with min 30% overlap, which will ask more shots and one more row.